SMTL ID : 7o1s.1

Complex-B bound [FeFe]-hydrogenase maturase HydE fromT. Maritima (Wild-type protein)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

1 x CYS: CYSTEINE(Non-covalent)

CYS.1: 12 residues within 4Å: Chain A: Q.107, R.159, T.268, T.269, A.270, L.305, Y.306 Ligands: FE2.2, CMO.3, CMO.4, CYN.5, SAH.15 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.269, A:T.269, A:T.269, A:A.270, A:Y.306 Water bridges: A:R.159, A:R.159 Salt bridges: A:R.159

1 x FE2: FE (II) ION(Non-functional Binders)

FE2.2: 4 residues within 4Å: Ligands: CYS.1, CMO.3, CMO.4, CYN.5 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: CYS.1, CYS.1

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.3: 8 residues within 4Å: Chain A: I.56, Q.107, L.157, M.291 Ligands: CYS.1, FE2.2, CMO.4, CYN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.107 CMO.4: 8 residues within 4Å: Chain A: L.157, G.226, P.266, T.268 Ligands: CYS.1, FE2.2, CMO.3, CYN.5 No protein-ligand interaction detected (PLIP)

1 x CYN: CYANIDE ION(Non-covalent)

CYN.5: 7 residues within 4Å: Chain A: T.268, T.269, M.291 Ligands: CYS.1, FE2.2, CMO.3, CMO.4 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: C.1, A:T.269, A:T.269

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.6: 8 residues within 4Å: Chain A: R.279, C.311, E.314, C.319, C.322, V.323 Ligands: H2S.7, H2S.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.311, A:C.319, A:C.322, H2O.11

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.7: 4 residues within 4Å: Chain A: C.311, E.314, C.319 Ligands: FES.6 No protein-ligand interaction detected (PLIP) H2S.8: 4 residues within 4Å: Chain A: R.279, C.322, M.326 Ligands: FES.6 No protein-ligand interaction detected (PLIP)

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.9: 9 residues within 4Å: Chain A: C.63, K.65, C.67, Y.69, C.70, L.72, R.73, G.109 Ligands: SAH.15 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:E.110 Metal complexes: A:C.63, A:C.67, A:C.70

5 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.10: 6 residues within 4Å: Chain A: V.97, Q.98, F.99, G.100, M.324 Ligands: CPS.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.98, A:F.99 Hydrogen bonds: A:Q.98 CPS.11: 7 residues within 4Å: Chain A: E.33, F.36, K.37, D.40, R.284 Ligands: CPS.12, CPS.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.36, A:R.284 Hydrogen bonds: A:D.40 Water bridges: A:E.33, A:R.284 CPS.12: 8 residues within 4Å: Chain A: R.29, E.33, F.246, T.247, L.250, I.281 Ligands: CPS.11, CPS.13 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.246, A:L.250, A:I.281 Hydrogen bonds: A:R.29, A:E.33, A:E.33, A:T.247 Water bridges: A:R.29 CPS.13: 3 residues within 4Å: Chain A: R.29 Ligands: CPS.11, CPS.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29 Water bridges: A:R.29 CPS.14: 3 residues within 4Å: Chain A: P.321, E.328 Ligands: CPS.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.321, A:E.328

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.15: 19 residues within 4Å: Chain A: Y.69, C.70, Q.107, S.108, G.109, S.136, G.138, R.159, E.161, R.180, M.199, P.229, F.230, I.231, Y.303, L.305, Y.306 Ligands: CYS.1, SF4.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Q.107 Hydrogen bonds: A:E.161, A:I.231, A:I.231 Water bridges: A:G.138, A:R.159, A:R.159, A:E.161, A:E.161, A:R.180, A:R.180, A:R.180 Salt bridges: A:R.180

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.16: 3 residues within 4Å: Chain A: R.54, T.134, R.155 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rohac, R. et al., Crystal Structure of the [FeFe]-Hydrogenase Maturase HydE Bound to Complex-B. J.Am.Chem.Soc. (2021)

Release Date

2021-05-26

Peptides

[FeFe] hydrogenase maturase subunit HydE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

[FeFe] hydrogenase maturase subunit HydE

Related Entries With Identical Sequence